@@ -1,8 +1,8 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

-Version: 2.1.1

-Date: 2019-10-12

+Version: 2.3.1

+Date: 2019-10-22

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

@@ -1,6 +1,7 @@

 CHANGES in VERSION 2.3.1

 * `anno_points()`: allows images as symbols.

+* add `HEATMAP_LEGEND_PADDING` and `ANNOTATION_LEGEND_PADDING` options in `ht_opt`

 ========================

@@ -2802,6 +2802,10 @@ anno_mark = function(at, labels, which = c("column", "row"),

 	labels_rot = labels_rot %% 360

+	if(!inherits(padding, "unit")) {

+		padding = convertHeight(padding*grobHeight(textGrob("a", gp = subset_gp(labels_gp, 1))), "mm")

+	}

+

 	# a map between row index and positions

 	# pos_map = 

 	row_fun = function(index) {

@@ -909,25 +909,25 @@ setMethod(f = "make_layout",

     object@heatmap_legend_param$side = heatmap_legend_side   

     if(show_heatmap_legend) {

         if(heatmap_legend_side == "top") {

-            object@heatmap_legend_param$padding = unit(c(2, 0, 0, 0), "mm")

+            object@heatmap_legend_param$padding = unit.c(ht_opt$HEATMAP_LEGEND_PADDING, unit(c(0, 0, 0), "mm")) #unit(c(2, 0, 0, 0), "mm")

             size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_width = calc_legends_max_width(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_top_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, heatmap_legend_top = heatmap_list_layout_index("heatmap_legend_top"))

         } else if(heatmap_legend_side == "bottom") {

-            object@heatmap_legend_param$padding = unit(c(0, 0, 2, 0), "mm")

+            object@heatmap_legend_param$padding = unit.c(unit(c(0, 0), "mm"), ht_opt$HEATMAP_LEGEND_PADDING, unit(0, "mm")) # unit(c(0, 0, 2, 0), "mm")

             size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_width = calc_legends_max_width(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_bottom_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, heatmap_legend_bottom = heatmap_list_layout_index("heatmap_legend_bottom"))

         } else if(heatmap_legend_side == "left") {

-            object@heatmap_legend_param$padding = unit(c(0, 0, 0, 2), "mm")

+            object@heatmap_legend_param$padding = unit.c(unit(c(0, 0, 0), "mm"), ht_opt$HEATMAP_LEGEND_PADDING) # unit(c(0, 0, 0, 2), "mm")

             size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_height = calc_legends_max_height(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_left_width = size[1]

             object@layout$layout_index = rbind(object@layout$layout_index, heatmap_legend_left = heatmap_list_layout_index("heatmap_legend_left"))

         } else if(heatmap_legend_side == "right") {

-            object@heatmap_legend_param$padding = unit(c(0, 2, 0, 0), "mm")

+            object@heatmap_legend_param$padding = unit.c(unit(0, "mm"), ht_opt$HEATMAP_LEGEND_PADDING, unit(c(0, 0), "mm")) # unit(c(0, 2, 0, 0), "mm")

             size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_height = calc_legends_max_height(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_right_width = size[1]

@@ -980,25 +980,25 @@ setMethod(f = "make_layout",

     object@annotation_legend_param$side = annotation_legend_side

     if(show_annotation_legend) {

         if(annotation_legend_side == "top") {

-            object@annotation_legend_param$padding = unit(c(2, 0, 0, 0), "mm")

+            object@annotation_legend_param$padding = unit.c(ht_opt$ANNOTATION_LEGEND_PADDING, unit(c(0, 0, 0), "mm")) # unit(c(2, 0, 0, 0), "mm")

             size = annotation_legend_size(object, legend_list = annotation_legend_list, max_width = calc_legends_max_width(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_top_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, annotation_legend_top = heatmap_list_layout_index("annotation_legend_top"))

         } else if(annotation_legend_side == "bottom") {

-            object@annotation_legend_param$padding = unit(c(0, 0, 2, 0), "mm")

+            object@annotation_legend_param$padding = unit.c(unit(c(0, 0), "mm"), ht_opt$ANNOTATION_LEGEND_PADDING, unit(0, "mm")) # unit(c(0, 0, 2, 0), "mm")

             size = annotation_legend_size(object, legend_list = annotation_legend_list, max_width = calc_legends_max_width(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_bottom_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, annotation_legend_bottom = heatmap_list_layout_index("annotation_legend_bottom"))

         } else if(annotation_legend_side == "left") {

-            object@annotation_legend_param$padding = unit(c(0, 0, 0, 2), "mm")

+            object@annotation_legend_param$padding = unit.c(unit(c(0, 0, 0), "mm"), ht_opt$ANNOTATION_LEGEND_PADDING) # unit(c(0, 0, 0, 2), "mm")

             size = annotation_legend_size(object, legend_list = annotation_legend_list, max_height = calc_legends_max_height(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_left_width = size[1]

             object@layout$layout_index = rbind(object@layout$layout_index, annotation_legend_left = heatmap_list_layout_index("annotation_legend_left"))

         } else if(annotation_legend_side == "right") {

-            object@annotation_legend_param$padding = unit(c(0, 2, 0, 0), "mm")

+            object@annotation_legend_param$padding = unit.c(unit(0, "mm"), ht_opt$ANNOTATION_LEGEND_PADDING, unit(c(0, 0), "mm")) # unit(c(0, 2, 0, 0), "mm")

             size = annotation_legend_size(object, legend_list = annotation_legend_list, max_height = calc_legends_max_height(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_right_width = size[1]

@@ -40,9 +40,9 @@ make_comb_mat_from_matrix = function(x, mode, top_n_sets = Inf, min_set_size = -

 	set_size = set_size[l]

 	x = x[, l, drop = FALSE]

-	if(ncol(x) > 15) {

-		stop_wrap("Currently number of sets <= 15 is only supported.")

-	}

+	# if(ncol(x) > 15) {

+	# 	stop_wrap("Currently number of sets <= 15 is only supported.")

+	# }

 	if(is.null(rownames(x))) {

 		x_has_rownames = FALSE

@@ -44,6 +44,8 @@

 # -TITLE_PADDING space between row/column titles and heatmap body.

 # -COLUMN_ANNO_PADDING space between column annotations and heatmap body.

 # -ROW_ANNO_PADDING space between row annotations and heatmap body.

+# -HEATMAP_LEGEND_PADDING space between heatmap legends and heatmaps

+# -ANNOTATION_LEGEND_PADDING space between annotation legends and heatmaps

 #

 # Other parameters:

 #

@@ -150,6 +152,14 @@ ht_opt = setGlobalOptions(

 	ROW_ANNO_PADDING = list(

 		.value = unit(1, "mm"),

 		.class = "unit"

+	),

+	HEATMAP_LEGEND_PADDING = list(

+		.value = unit(2, "mm"),

+		.class = "unit"

+	),

+	ANNOTATION_LEGEND_PADDING = list(

+		.value = unit(2, "mm"),

+		.class = "unit"

 	)

 )

@@ -7,11 +7,12 @@ Names of the Combination sets

 Names of the Combination sets

 }

 \usage{

-comb_name(m)

+comb_name(m, readable = FALSE)

 }

 \arguments{

   \item{m}{A combination matrix returned by \code{\link{make_comb_mat}}.}

+  \item{readable}{Whether the combination represents as e.g. "A&B&C".}

 }

 \details{

@@ -31,4 +32,5 @@ lt = list(a = sample(letters, 10),

           c = sample(letters, 20))

 m = make_comb_mat(lt)

 comb_name(m)

+comb_name(m, readable = TRUE)

 }

@@ -59,6 +59,8 @@ Following parameters control the space between heatmap components:

   \item{TITLE_PADDING}{space between row/column titles and heatmap body.}

   \item{COLUMN_ANNO_PADDING}{space between column annotations and heatmap body.}

   \item{ROW_ANNO_PADDING}{space between row annotations and heatmap body.}

+  \item{HEATMAP_LEGEND_PADDING}{space between heatmap legends and heatmaps}

+  \item{ANNOTATION_LEGEND_PADDING}{space between annotation legends and heatmaps}

 }

 Other parameters: